Actually, I just found this [ https://issues.apache.org/jira/browse/SPARK-1680], which after a bit of googling and reading leads me to believe that the preferred way to change the yarn environment is to edit the spark-defaults.conf file by adding this line: spark.yarn.appMasterEnv.PYSPARK_PYTHON /path/to/python
While both this solution and the solution from my prior email work, I believe this is the preferred solution. Sorry for the flurry of emails. Again, thanks for all the help! Andrew On Fri, Jan 15, 2016 at 1:47 PM, Andrew Weiner < andrewweiner2...@u.northwestern.edu> wrote: > I finally got the pi.py example to run in yarn cluster mode. This was the > key insight: > https://issues.apache.org/jira/browse/SPARK-9229 > > I had to set SPARK_YARN_USER_ENV in spark-env.sh: > export SPARK_YARN_USER_ENV="PYSPARK_PYTHON=/home/aqualab/local/bin/python" > > This caused the PYSPARK_PYTHON environment variable to be used in my yarn > environment in cluster mode. > > Thank you for all your help! > > Best, > Andrew > > > > On Fri, Jan 15, 2016 at 12:57 PM, Andrew Weiner < > andrewweiner2...@u.northwestern.edu> wrote: > >> I tried playing around with my environment variables, and here is an >> update. >> >> When I run in cluster mode, my environment variables do not persist >> throughout the entire job. >> For example, I tried creating a local copy of HADOOP_CONF_DIR in >> /home/<username>/local/etc/hadoop/conf, and then, in spark-env.sh I the >> variable: >> export HADOOP_CONF_DIR=/home/<username>/local/etc/hadoop/conf >> >> Later, when we print the environment variables in the python code, I see >> this: >> >> ('HADOOP_CONF_DIR', '/etc/hadoop/conf') >> >> However, when I run in client mode, I see this: >> >> ('HADOOP_CONF_DIR', '/home/awp066/local/etc/hadoop/conf') >> >> Furthermore, if I omit that environment variable from spark-env.sh >> altogether, I get the expected error in both client and cluster mode: >> >> When running with master 'yarn' >> either HADOOP_CONF_DIR or YARN_CONF_DIR must be set in the environment. >> >> This suggests that my environment variables are being used when I first >> submit the job, but at some point during the job, my environment variables >> are thrown out and someone's (yarn's?) environment variables are being used. >> >> Andrew >> >> >> On Fri, Jan 15, 2016 at 11:03 AM, Andrew Weiner < >> andrewweiner2...@u.northwestern.edu> wrote: >> >>> Indeed! Here is the output when I run in cluster mode: >>> >>> Traceback (most recent call last): >>> File "pi.py", line 22, in ? >>> raise RuntimeError("\n"+str(sys.version_info) +"\n"+ >>> RuntimeError: >>> (2, 4, 3, 'final', 0) >>> [('PYSPARK_GATEWAY_PORT', '48079'), ('PYTHONPATH', >>> '/scratch2/hadoop/yarn/local/usercache/<username>/filecache/116/spark-assembly-1.6.0-hadoop2.4.0.jar:/home/<user>/spark-1.6.0-bin-hadoop2.4/python:/home/<username>/code/libs:/scratch5/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0239/container_1450370639491_0239_01_000001/pyspark.zip:/scratch5/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0239/container_1450370639491_0239_01_000001/py4j-0.9-src.zip'), >>> ('PYTHONUNBUFFERED', 'YES')] >>> >>> As we suspected, it is using Python 2.4 >>> >>> One thing that surprises me is that PYSPARK_PYTHON is not showing up in the >>> list, even though I am setting it and exporting it in spark-submit *and* in >>> spark-env.sh. Is there somewhere else I need to set this variable? Maybe >>> in one of the hadoop conf files in my HADOOP_CONF_DIR? >>> >>> Andrew >>> >>> >>> >>> On Thu, Jan 14, 2016 at 1:14 PM, Bryan Cutler <cutl...@gmail.com> wrote: >>> >>>> It seems like it could be the case that some other Python version is >>>> being invoked. To make sure, can you add something like this to the top of >>>> the .py file you are submitting to get some more info about how the >>>> application master is configured? >>>> >>>> import sys, os >>>> raise RuntimeError("\n"+str(sys.version_info) +"\n"+ >>>> str([(k,os.environ[k]) for k in os.environ if "PY" in k])) >>>> >>>> On Thu, Jan 14, 2016 at 8:37 AM, Andrew Weiner < >>>> andrewweiner2...@u.northwestern.edu> wrote: >>>> >>>>> Hi Bryan, >>>>> >>>>> I ran "$> python --version" on every node on the cluster, and it is >>>>> Python 2.7.8 for every single one. >>>>> >>>>> When I try to submit the Python example in client mode >>>>> * ./bin/spark-submit --master yarn --deploy-mode client >>>>> --driver-memory 4g --executor-memory 2g --executor-cores 1 >>>>> ./examples/src/main/python/pi.py 10* >>>>> That's when I get this error that I mentioned: >>>>> >>>>> 16/01/14 10:09:10 WARN scheduler.TaskSetManager: Lost task 0.0 in >>>>> stage 0.0 (TID 0, mundonovo-priv): org.apache.spark.SparkException: >>>>> Error from python worker: >>>>> python: module pyspark.daemon not found >>>>> PYTHONPATH was: >>>>> >>>>> /scratch5/hadoop/yarn/local/usercache/<username>/filecache/48/spark-assembly-1.6.0-hadoop2.4.0.jar:/home/aqualab/spark-1.6.0-bin-hadoop2.4/python:/home/jpr123/hg.pacific/python-common:/home/jp >>>>> >>>>> r123/python-libs:/home/jpr123/lib/python2.7/site-packages:/home/zsb739/local/lib/python2.7/site-packages:/home/jpr123/mobile-cdn-analysis:/home/<username>/lib/python2.7/site-packages:/home/<username>/code/libs:/scratch5/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0187/container_1450370639491_0187_01_000002/pyspark.zip:/scratch5/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0187/container_1450370639491_0187_01_000002/py4j-0.9-src.zip >>>>> java.io.EOFException >>>>> at java.io.DataInputStream.readInt(DataInputStream.java:392) >>>>> at >>>>> org.apache.spark.api.python.PythonWorkerFactory.startDaemon(PythonWorkerFactory.scala:164) >>>>> at [....] >>>>> >>>>> followed by several more similar errors that also say: >>>>> Error from python worker: >>>>> python: module pyspark.daemon not found >>>>> >>>>> >>>>> Even though the default python appeared to be correct, I just went >>>>> ahead and explicitly set PYSPARK_PYTHON in conf/spark-env.sh to the path >>>>> of >>>>> the default python binary executable. After making this change I was able >>>>> to run the job successfully in client! That is, this appeared to fix the >>>>> "pyspark.daemon not found" error when running in client mode. >>>>> >>>>> However, when running in cluster mode, I am still getting the same >>>>> syntax error: >>>>> >>>>> Traceback (most recent call last): >>>>> File "pi.py", line 24, in ? >>>>> from pyspark import SparkContext >>>>> File >>>>> "/home/<username>/spark-1.6.0-bin-hadoop2.4/python/pyspark/__init__.py", >>>>> line 61 >>>>> indent = ' ' * (min(len(m) for m in indents) if indents else 0) >>>>> ^ >>>>> SyntaxError: invalid syntax >>>>> >>>>> Is it possible that the PYSPARK_PYTHON environment variable is ignored >>>>> when jobs are submitted in cluster mode? It seems that Spark or Yarn is >>>>> going behind my back, so to speak, and using some older version of python >>>>> I didn't even know was installed. >>>>> >>>>> Thanks again for all your help thus far. We are getting close.... >>>>> >>>>> Andrew >>>>> >>>>> >>>>> >>>>> On Wed, Jan 13, 2016 at 6:13 PM, Bryan Cutler <cutl...@gmail.com> >>>>> wrote: >>>>> >>>>>> Hi Andrew, >>>>>> >>>>>> There are a couple of things to check. First, is Python 2.7 the >>>>>> default version on all nodes in the cluster or is it an alternate >>>>>> install? >>>>>> Meaning what is the output of this command "$> python --version" If it >>>>>> is >>>>>> an alternate install, you could set the environment variable " >>>>>> PYSPARK_PYTHON" Python binary executable to use for PySpark in both >>>>>> driver and workers (default is python). >>>>>> >>>>>> Did you try to submit the Python example under client mode? >>>>>> Otherwise, the command looks fine, you don't use the --class option for >>>>>> submitting python files >>>>>> * ./bin/spark-submit --master yarn --deploy-mode client >>>>>> --driver-memory 4g --executor-memory 2g --executor-cores 1 >>>>>> ./examples/src/main/python/pi.py 10* >>>>>> >>>>>> That is a good sign that local jobs and Java examples work, probably >>>>>> just a small configuration issue :) >>>>>> >>>>>> Bryan >>>>>> >>>>>> On Wed, Jan 13, 2016 at 3:51 PM, Andrew Weiner < >>>>>> andrewweiner2...@u.northwestern.edu> wrote: >>>>>> >>>>>>> Thanks for your continuing help. Here is some additional info. >>>>>>> >>>>>>> *OS/architecture* >>>>>>> output of *cat /proc/version*: >>>>>>> Linux version 2.6.18-400.1.1.el5 ( >>>>>>> mockbu...@x86-012.build.bos.redhat.com) >>>>>>> >>>>>>> output of *lsb_release -a*: >>>>>>> LSB Version: >>>>>>> >>>>>>> :core-4.0-amd64:core-4.0-ia32:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-ia32:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-ia32:printing-4.0-noarch >>>>>>> Distributor ID: RedHatEnterpriseServer >>>>>>> Description: Red Hat Enterprise Linux Server release 5.11 >>>>>>> (Tikanga) >>>>>>> Release: 5.11 >>>>>>> Codename: Tikanga >>>>>>> >>>>>>> *Running a local job* >>>>>>> I have confirmed that I can successfully run python jobs using >>>>>>> bin/spark-submit --master local[*] >>>>>>> Specifically, this is the command I am using: >>>>>>> *./bin/spark-submit --master local[8] >>>>>>> ./examples/src/main/python/wordcount.py >>>>>>> file:/home/<username>/spark-1.6.0-bin-hadoop2.4/README.md* >>>>>>> And it works! >>>>>>> >>>>>>> *Additional info* >>>>>>> I am also able to successfully run the Java SparkPi example using >>>>>>> yarn in cluster mode using this command: >>>>>>> * ./bin/spark-submit --class org.apache.spark.examples.SparkPi >>>>>>> --master yarn --deploy-mode cluster --driver-memory 4g >>>>>>> --executor-memory 2g --executor-cores 1 lib/spark-examples*.jar >>>>>>> 10* >>>>>>> This Java job also runs successfully when I change --deploy-mode to >>>>>>> client. The fact that I can run Java jobs in cluster mode makes me >>>>>>> thing >>>>>>> that everything is installed correctly--is that a valid assumption? >>>>>>> >>>>>>> The problem remains that I cannot submit python jobs. Here is the >>>>>>> command that I am using to try to submit python jobs: >>>>>>> * ./bin/spark-submit --master yarn --deploy-mode cluster >>>>>>> --driver-memory 4g --executor-memory 2g --executor-cores 1 >>>>>>> ./examples/src/main/python/pi.py 10* >>>>>>> Does that look like a correct command? I wasn't sure what to put >>>>>>> for --class so I omitted it. At any rate, the result of the above >>>>>>> command >>>>>>> is a syntax error, similar to the one I posted in the original email: >>>>>>> >>>>>>> Traceback (most recent call last): >>>>>>> File "pi.py", line 24, in ? >>>>>>> from pyspark import SparkContext >>>>>>> File >>>>>>> "/home/<username>/spark-1.6.0-bin-hadoop2.4/python/pyspark/__init__.py", >>>>>>> line 61 >>>>>>> indent = ' ' * (min(len(m) for m in indents) if indents else 0) >>>>>>> ^ >>>>>>> SyntaxError: invalid syntax >>>>>>> >>>>>>> >>>>>>> This really looks to me like a problem with the python version. >>>>>>> Python 2.4 would throw this syntax error but Python 2.7 would not. And >>>>>>> yet >>>>>>> I am using Python 2.7.8. Is there any chance that Spark or Yarn is >>>>>>> somehow >>>>>>> using an older version of Python without my knowledge? >>>>>>> >>>>>>> Finally, when I try to run the same command in client mode... >>>>>>> * ./bin/spark-submit --master yarn --deploy-mode client >>>>>>> --driver-memory 4g --executor-memory 2g --executor-cores 1 >>>>>>> ./examples/src/main/python/pi.py 10* >>>>>>> I get the error I mentioned in the prior email: >>>>>>> Error from python worker: >>>>>>> python: module pyspark.daemon not found >>>>>>> >>>>>>> Any thoughts? >>>>>>> >>>>>>> Best, >>>>>>> Andrew >>>>>>> >>>>>>> >>>>>>> On Mon, Jan 11, 2016 at 12:25 PM, Bryan Cutler <cutl...@gmail.com> >>>>>>> wrote: >>>>>>> >>>>>>>> This could be an environment issue, could you give more details >>>>>>>> about the OS/architecture that you are using? If you are sure >>>>>>>> everything >>>>>>>> is installed correctly on each node following the guide on "Running >>>>>>>> Spark >>>>>>>> on Yarn" http://spark.apache.org/docs/latest/running-on-yarn.html >>>>>>>> and that the spark assembly jar is reachable, then I would check to >>>>>>>> see if >>>>>>>> you can submit a local job to just run on one node. >>>>>>>> >>>>>>>> On Fri, Jan 8, 2016 at 5:22 PM, Andrew Weiner < >>>>>>>> andrewweiner2...@u.northwestern.edu> wrote: >>>>>>>> >>>>>>>>> Now for simplicity I'm testing with wordcount.py from the provided >>>>>>>>> examples, and using Spark 1.6.0 >>>>>>>>> >>>>>>>>> The first error I get is: >>>>>>>>> >>>>>>>>> 16/01/08 19:14:46 ERROR lzo.GPLNativeCodeLoader: Could not load >>>>>>>>> native gpl library >>>>>>>>> java.lang.UnsatisfiedLinkError: no gplcompression in >>>>>>>>> java.library.path >>>>>>>>> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864) >>>>>>>>> at [....] >>>>>>>>> >>>>>>>>> A bit lower down, I see this error: >>>>>>>>> >>>>>>>>> 16/01/08 19:14:48 WARN scheduler.TaskSetManager: Lost task 0.0 in >>>>>>>>> stage 0.0 (TID 0, mundonovo-priv): org.apache.spark.SparkException: >>>>>>>>> Error from python worker: >>>>>>>>> python: module pyspark.daemon not found >>>>>>>>> PYTHONPATH was: >>>>>>>>> >>>>>>>>> /scratch5/hadoop/yarn/local/usercache/<username>/filecache/22/spark-assembly-1.6.0-hadoop2.4.0.jar:/home/jpr123/hg.pacific/python-common:/home/jpr123/python-libs:/home/jpr123/lib/python2.7/site-packages:/home/zsb739/local/lib/python2.7/site-packages:/home/jpr123/mobile-cdn-analysis:/home/<username>/lib/python2.7/site-packages:/scratch4/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0136/container_1450370639491_0136_01_000002/pyspark.zip:/scratch4/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0136/container_1450370639491_0136_01_000002/py4j-0.9-src.zip >>>>>>>>> java.io.EOFException >>>>>>>>> at >>>>>>>>> java.io.DataInputStream.readInt(DataInputStream.java:392) >>>>>>>>> at [....] >>>>>>>>> >>>>>>>>> And then a few more similar pyspark.daemon not found errors... >>>>>>>>> >>>>>>>>> Andrew >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Jan 8, 2016 at 2:31 PM, Bryan Cutler <cutl...@gmail.com> >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hi Andrew, >>>>>>>>>> >>>>>>>>>> I know that older versions of Spark could not run PySpark on YARN >>>>>>>>>> in cluster mode. I'm not sure if that is fixed in 1.6.0 though. >>>>>>>>>> Can you >>>>>>>>>> try setting deploy-mode option to "client" when calling spark-submit? >>>>>>>>>> >>>>>>>>>> Bryan >>>>>>>>>> >>>>>>>>>> On Thu, Jan 7, 2016 at 2:39 PM, weineran < >>>>>>>>>> andrewweiner2...@u.northwestern.edu> wrote: >>>>>>>>>> >>>>>>>>>>> Hello, >>>>>>>>>>> >>>>>>>>>>> When I try to submit a python job using spark-submit (using >>>>>>>>>>> --master yarn >>>>>>>>>>> --deploy-mode cluster), I get the following error: >>>>>>>>>>> >>>>>>>>>>> /Traceback (most recent call last): >>>>>>>>>>> File "loss_rate_by_probe.py", line 15, in ? >>>>>>>>>>> from pyspark import SparkContext >>>>>>>>>>> File >>>>>>>>>>> >>>>>>>>>>> "/scratch5/hadoop/yarn/local/usercache/<username>/filecache/18/spark-assembly-1.3.1-hadoop2.4.0.jar/pyspark/__init__.py", >>>>>>>>>>> line 41, in ? >>>>>>>>>>> File >>>>>>>>>>> >>>>>>>>>>> "/scratch5/hadoop/yarn/local/usercache/<username>/filecache/18/spark-assembly-1.3.1-hadoop2.4.0.jar/pyspark/context.py", >>>>>>>>>>> line 219 >>>>>>>>>>> with SparkContext._lock: >>>>>>>>>>> ^ >>>>>>>>>>> SyntaxError: invalid syntax/ >>>>>>>>>>> >>>>>>>>>>> This is very similar to this post from 2014 >>>>>>>>>>> < >>>>>>>>>>> http://apache-spark-user-list.1001560.n3.nabble.com/SparkContext-lock-Error-td18233.html >>>>>>>>>>> > >>>>>>>>>>> , but unlike that person I am using Python 2.7.8. >>>>>>>>>>> >>>>>>>>>>> Here is what I'm using: >>>>>>>>>>> Spark 1.3.1 >>>>>>>>>>> Hadoop 2.4.0.2.1.5.0-695 >>>>>>>>>>> Python 2.7.8 >>>>>>>>>>> >>>>>>>>>>> Another clue: I also installed Spark 1.6.0 and tried to submit >>>>>>>>>>> the same >>>>>>>>>>> job. I got a similar error: >>>>>>>>>>> >>>>>>>>>>> /Traceback (most recent call last): >>>>>>>>>>> File "loss_rate_by_probe.py", line 15, in ? >>>>>>>>>>> from pyspark import SparkContext >>>>>>>>>>> File >>>>>>>>>>> >>>>>>>>>>> "/scratch5/hadoop/yarn/local/usercache/<username>/appcache/application_1450370639491_0119/container_1450370639491_0119_01_000001/pyspark.zip/pyspark/__init__.py", >>>>>>>>>>> line 61 >>>>>>>>>>> indent = ' ' * (min(len(m) for m in indents) if indents else >>>>>>>>>>> 0) >>>>>>>>>>> ^ >>>>>>>>>>> SyntaxError: invalid syntax/ >>>>>>>>>>> >>>>>>>>>>> Any thoughts? >>>>>>>>>>> >>>>>>>>>>> Andrew >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> View this message in context: >>>>>>>>>>> http://apache-spark-user-list.1001560.n3.nabble.com/SparkContext-SyntaxError-invalid-syntax-tp25910.html >>>>>>>>>>> Sent from the Apache Spark User List mailing list archive at >>>>>>>>>>> Nabble.com. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> --------------------------------------------------------------------- >>>>>>>>>>> To unsubscribe, e-mail: user-unsubscr...@spark.apache.org >>>>>>>>>>> For additional commands, e-mail: user-h...@spark.apache.org >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
